From 2a6bd3bd9f34b22f7648d4d1c3f898c032ee81fc Mon Sep 17 00:00:00 2001 From: JLSteenwyk Date: Tue, 24 Oct 2023 15:05:22 -0700 Subject: [PATCH] initial testing of new python and biopython versions --- .DS_Store | Bin 6148 -> 6148 bytes requirements.txt | 17 ++- setup.py | 2 +- ...10.renamed.fa.mafft.clipkit.orthosnap.4.fa | 118 +++++++++--------- 4 files changed, 74 insertions(+), 63 deletions(-) diff --git a/.DS_Store b/.DS_Store index 4a92185e598a0cdb80d93c00aaea3cfdd51dfba2..3c76d7fa9f0cd3489892fcfa187ac702d0371ae3 100644 GIT binary patch delta 186 zcmZoMXfc@J&&aYdU^gQp%VZv=KQ`y7CTK2X7Y~VxqpRo1r-iqFo;&CBlsnhFGrj1ZcE7fQpZZXg52J)6HX$*^o@ I=lIJH0MGs@3jhEB delta 33 pcmZoMXfc@J&&aefU^nAr0}+Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_09150-RA -MGSMHEAG---------------------------------------------------- +>Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate +M----------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ -----------------------SRPAADAD---MDTDR------VHPEAV---------- ------SNSERDFEKQDSKPEYRDAFGDEEYAEVKYKTLSWWQCGFLMVAETVSLGILSLP -AVV---AALGLVPAIILLVALGLMSTYTGYTIGQFKWAYPHIHSMGDAGEVIMGRFGREL -FGTGQLLLVVFIMASHILTFTVAMNSITDHGTCSIVFGVVGLVISFVLCLPRTLAKVSFL -SVASFISVFSAVLIVMIAVGVQRPWHGSVNATVDTSLYKAFLAVCNIVFSFCRLFLHFIS -FMDRTDRTAGHVAFFGFMAELRNPRDYPKSLFLLQGIDTCLYIVAAVVIYCYAGDDVTSP -ALGSASTIVKKVAYGIALPTIIIGGVVNGHVACKYIYVRMWR-HSDRMHKRDLVATGSWV -LIGLATWIVAWIIAEAIPVFNNLLSLVASLFASWFTYGFSALFWLYLNKGRFFSTPMKTA -LTILNVVIMGIACCICGLGLYVSGKALHDDPSSASF------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------SCANNA--------------------------- +FGIGQLLFLIFLMASHILTFTVVFNTITNHGTCTIVFGVVGLVVSFIGALPRTMGKVYWM +SMASCISIVTATVVTMIAIGVQAPDHVHVDATTEVSFQDAFLAVTNIIFAY--------- +--------IAHVAFFGFISEMHDPRDFPKSLTMLQVVDTSLYIVTAMVIYRYAGPDVASP +ALSSAGPLMKKVAYGLAIPTVVIAGVVFGHVACKYIYVRIFR-GSAHMHQNSFLAIGSWV +AIALGVWVVAWVIAESIPVFNELLSLISSLFGSWFSYGLPAIFWLVMNKGRWFSTRSKIC +LTIVNFLILAFACALCGMGLYVSGKSIHDSSSKASW------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ->Aspergillus_fumigatus_Af293|EAL84262.1 -MGSMHEAG---------------------------------------------------- +---------------------------TCKNNAT-------------------------- ------------------------------------------------------------ ------------------------------------------------------------ -----------------------SRPAAGAD---MDTDR------VHPEAV---------- ------SDNERDFEKQDSKPEYQDAFGDEEYAEVKYKTLSWC------------------- +----------------------------------------------------------TT +>Aspergillus_fumigatus_Af293|EAL85095.2-duplicate +M---------------------MLWLK--------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ --------VFSAVLIVMIAVGVQRPWHGGLNATVDTNLYKAFLAVCNIVFSFCRLFLHFSS -FMDRTNKTAGHVAFFGFMAELRNPRDYPKSLFLLQGIDTCLYIIAAVVIYCYAGDDVTSP -ALGSASTIVKKVAYGIALPTIIIGGVVNGHVACKYIYVRMWR-HSDRMHKRDLVATGSWV -LIGLATWIVAWIIAEAIPVFNNLLSLVREVLVV-----ICTMIW-----ERVLIAPSVTA -FRLF------------PLALFVATR----DPRSIG------------------------- +--------------------RRNMLMGRRQMTRLEM------------------------ +-------------------------KNAERSNIV-------SCRGVMVAENISLGILSLS +SAV---ATLGIVPAVILLLGLSAISWYTGYIMGQFKLRFPQIHSMGDAGELLMGRFGREL +FGIGQLLFLIFLMASHILTFSVVFNTITNHGTCTIVFGVVGLVVSFIGALPRTMGKVYWM +SMASCISIVTATVVTMIAIGVQAPDHVHVNVTTKVSFQDAFLAVTNIIFAY--------- +--------IAHVAFFGFISEMHDPRDFPKSLTMLQVVDTSLYIVTAMVIYRYAGPDVASP +ALSSAGPLMKKVAYGLAIPTVVIAGVVFGHVACKYIYVRIFR-GSAHMHQNSFLAIGSWV +AIALGVWVVAWVIAESIPVFNELLSLISSLFGSWFSYGLPAIFWLVMNKGRWFSTRSKIC +LTIVNFFILAFACALCGMGLYVSGKSIHDSSSKASW------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ +---------------------------TCKNNAT-------------------------- ------------------------------------------------------------ ------------------------------------------------------------ +----------------------------------------------------------TT +>Aspergillus_fischeri_NRRL181|XP_001261692.1 +M----------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ->Aspergillus_fischeri_NRRL181|XP_001267441.1 -MGSMLEAG---------------------------------------------------- +-------------------------AVSRD---LEA----------PAVVNDP------- +---TAYDATVEKKEYADGTPANDPFGNEECGEVKYRVMSWWQCGTLMVAENISLGILSLP +SAV---ATLGIVPAVILLLGLSAISWYTGYIMGQFKLRFPQVHSMGDAGELLMGRFGREL +FGIGQLLFLIFLMASHILTFTVVFNTITNHGTCTIVFGVVGLVVSFIGALPRTMGKVYWM +SMASCISIVTATVVTMIAIGVQAPEHVHVDATTEVSFQDAFLAVTNIIFAY--------- +--------IAHVAFFGFISEMHDPRDFPKSLTMLQVVDTSLYIVTAMVIYRYAGPDVASP +ALSSAGPVMKKVAYGLAIPTVVIAGVVFGHVACKYIYVRIFR-GSAHMHQNSFLAIGSWV +AIALSVWVVAWVIAESIPVFNELLSLISSLFGSWFSYGLPAIFWLVMNKGRWFSTRSKIC +LTIVNFLILAFACALCGMGLYVSGKSIHDSSSKASW------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -----------------------SRPAADAE---MDTDR------VHPEAV---------- ------SDGERDFEKQDSKPEYQDAFGDEEYAEVKYKTLSWCH------GCRDSVTGYSLP -ASG---GGLGPCP---------------------FKWAYPHIHSMGDAGEVIMGRFGREL -FGTGQLLLVVFIMASHILTFTVAMNSITDHGTCSIVFGVVGLVISFVLCLPRTLAKVSFL -SVASFISVFSAVLIVMIAVGVQRPWHGSVNATVDTSLYKAFLAVCNIVFSF--------- ---------SGHVAFFGFMAELKNPRDYPKSLFLLQGIDTCLYIVAAVVIYCYAGDDVTSP -ALGSASIVVKKVAYGIALPTIIIGGVVNGHVACKYIYVRMWR-HSDRMHKRDLVATGSWV -LIGLATWIVAWIIAEAIPVFNNLLSLVASLFASWFTYGFSALFWLYLNKGRFFSTPMKTA -LTILNVVIMGIACCICGLGLYVSGKALHDDPSSASF------------------------ ------------------------------------------------------------ +---------------------------TCKNNAT-------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------SCANNA--------------------------- ------------------------------------------------------------ +>Aspergillus_niger_CBS_513.88|XP_001401336.1 +M----------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ->Aspergillus_niger_CBS_513.88|XP_001400898.1 -M--AHPTG---------------------------------------------------- +------------------------APTTRD---LEA----------LTVHHDS------- +-DIMADDLAEKKVSANESPPENDPFGNEECGEVKYRVMKWWHCGILMIAENISLGILSLP +SAV---ATLGIVPSIFLILGLSGISWYTGYVIGQFKLRYPQVHSMGDAGEILFGRIGREI +LFFGQLLFCIFLMSSHILTFTVLFNTITGHGTCTIVFGVVGLVVSFIGALPRTMGKVYWM +SLASCTSITVATIVTMVAIAMQAPDHVQVDITTHPSFSTAFLSVTNIVFAF--------- +--------IAHVAFFGFASEMEDPRDFPKSLAMLQVTDTTMYIVTAMVIYRYAGPDVASP +ALSSAGPLMSKVAYGLAIPTVIIAGVVFGHVASKYIYVRVWR-GSPQMHTNSLAAVGSWV +AIALGVWVIAWIIAESIPVFNDLLSLISSLFGSWFSYGLPAMFWLVMNRGQYTASPRKIF +LTIVNLVIFGIACAICGLGLYVSGKAIHDSSSSASW------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -----------------------DKVDSHLN---VQTGQFFQDGREEPYLH---------- -------DAEEKQDEKKGSPIYNDTFGDEEYAEVKYKVLSWWQCGFLMVAETVSLGILSLP -AVV---ATLGLAPAIVLIVGLGLLATYTGYVIGQFRWRYPHVQNLADAGEILFGSIGREI -FGIGQLLLVIFIMASHLLTFSVAMNTITEHGTCSIVFGVVGLVICFLLGLPRTSANVSYL -SVASFISVFSAVMIVMIAVGVERPYKGTLSATVDTSLYEAFLAVCNIVFSF--------- ---------SGHVAFFGFMSELKDHREYPKALCLLQGLDTILYLVTSVVIYIYAGPNVTSP -ALGSASELVGKVAYGIALPTIIIGGVVNGHVACKYVYVRIFR-HGDRMHSRDLLATGSWV -GIALGLWIIAWIIAEAIPVFNDLLSLIASLFASWSTFGFSGMFWLYLNKDRLFSSPRKIA -LTIFNVIIIGIAACICGLGLYVSGRSLHDDANGSSF------------------------ ------------------------------------------------------------ +---------------------------TCANNAST------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------SCASNA--------------------------- ------------------------------------------------------------ +>Aspergillus_awamori_IFM_58123|GCB19008.1 +M----------------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ->Aspergillus_awamori_IFM_58123|GCB19337.1 -M--AHPTG---------------------------------------------------- +------------------------APTTRD---LEA----------LAVHHDS------- +-DIMADDLAEKKVSANESPPENDPFGNEECGEVKYRVMKWWHCGILMIAENISLGILSLP +SAV---ATLGIVPSIFLILGLSGISWYTGYVIGQFKLRYPQVHSMGDAGEILFGRIGREI +LFFGQLLFCIFLMSSHILTFTVLFNTITGHGTCTIVFGVVGLVVSFIGALPRTMGKVYWM +SLASCTSITVATIVTMVAIAVQAPDHVQVDITTHPSFSTAFLSVTNIVFAF--------- +--------IAHVAFFGFASEMEDPRDFPKSLAMLQVTDTTMYIVTAMVIYRYAGPDVASP +ALSSAGPLMSKVAYGLAIPTVIIAGVVFGHVASKYIYVRVWR-GSPQMHTNSLAAVGSWV +AIALGVWVIAWIIAESIPVFNDLLSLISSLFGSWFSYGLPAMFWLVMNRGQYTASPRKIF +LTIVNLVIFGIACAICGLGLYVSGKAIHDSSSSASW------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -----------------------DKVDSHLN---VQTGQFFQDGREEPYLH---------- -------DAEEKQDEKKGSPIYNDTFGDEEYAEVKYKVLSWWQCGFLMVAETVSLGILSLP -AVV---ATLGLAPAIVLIVGLGLLATYTGYVIGQFRWRYPHVQNLADAGEILFGSIGREI -FGIGQLLLVIFIMASHLLTFSVAMNTITEHGTCSIVFGVVGLVICFLLGLPRTSANVSYL -SVASFISVFSAVMIVMIAVGVERPYKGTLSATVDTSLYEAFLAVCNIVFSF--------- ---------SGHVAFFGFMSELKDHREYPKALCLLQGLDTILYLVTSVVIYIYAGPNVTSP -ALGSASELVGKVAYGIALPTIIIGGVVNGHVACKYVYVRIFR-HGDRMHSRDLLATGSWV -GIALGLWIIAWIIAEAIPVFNDLLSLIASLFASWSTFGFSGMFWLYLNKDRLFSSPRKIA -LTFFNVIIIGIAACICGLGLYVSGRSLHDDANGSSF------------------------ ------------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------SCASNA--------------------------- +---------------------------TCANNAST------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------